Enzymatic reaction rate limits with constraints on equilibrium constants and experimental parameters

TLDR: A general methodology is presented for estimating maximum rates of enzymatic reactions based on general characteristics of enzyme reaction mechanisms, kinetic limits and thermodynamics and can be subject to additional constraints from experimental data, and thus conform to the distinctive features of the enzyme reaction.

Abstract: A general methodology is presented for estimating maximum rates of enzymatic reactions based on general characteristics of enzymatic reaction mechanisms, kinetic limits and thermodynamics. The useful range of experimentally derived kinetic parameters can also be extended by the methodology. The methodology divides the reaction mechanism into physical and chemical steps. Maximum rates that comply with kinetic and thermodynamic constraints are calculated by setting the physical rate constants to their diffusion limits and optimising the chemical rate constants subject to constraints of the reaction mechanism and overall equilibrium constant. Rate estimates from this methodology can be subject to additional constraints from experimental data, and thus conform to the distinctive features of the enzymatic reaction. The methodology is demonstrated using a reversible enzymatic reaction model involving ordered binding of two reactants and ordered release of two products (bi–bi mechanism). Numerical results are shown for alcohol dehydrogenase (EC 1.1.1.1), which has a bi–bi mechanism. Pyrophosphatase (EC 3.6.1.1) with a uni–bi mechanism and triosephosphate isomerase (EC 5.3.1.1) with a uni–uni mechanism are also examined.